Hi Kabeer,
You would add 2 join points. One for each AD (unless you have trust or AD relationship between them, then you don't need 2 join points). Once you have done that, you would add them in an 'Identity Store Sequence' under Administration -> Identity Management. Please note that the order listed there in the sequence, dictates the sequence how ISE would query a given store.
HTH
Hope that helps!
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